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Further Theoretical Considerations for Next-Generation Proteomics [article]

Magnus Palmblad
2021 bioRxiv   pre-print
In a recent Journal of Proteome Research paper, I described some general properties and constraints of a hypothetical next generation of proteomics technology based on single-molecule peptide sequencing. This work prompted many interesting questions, both from the reviewers of the initial manuscript and later from readers and colleagues. This follow-up paper addresses some of questions by clarifying the original results, considering alternative metrics, and a number of new simulations.
more » ... lly, the discriminative power of individual amino acids is revisited, simulating additional proteolytic agents. These simulations show allowing missed cleavages generally increases the discriminative power of the amino acids in the proteolytic motif. Additional simulations show the effect of non-ideal conditions modelled on the number of proteins lacking proteotypic reads is very small, and that the average number of proteotypic reads per protein follow the same rule on the performance of the optimal choice of labeled amino acids as the number of distinguishable proteins in NeXtProt. The goal of this paper is to expand prior results and continue the scientific discussion on the possibilities of future proteomics technologies.
doi:10.1101/2021.06.12.446585 fatcat:d6f32widijan3n6z44gtzrhjeu

D1.8 Tools Interoperability And Service Registry

Magnus Palmblad, Anna-Lena Lamprecht, Veit Schwämmle, Jon Ison
2018 Zenodo  
., Palmblad, M. Schwämmle, V. and Ison J.  ...  Community curation of software tools as illustrated for mass spectrometry based proteomics In preparation¨see https://tinyurl.com/proteomics-tools Palmblad, M., Lamprecht, A., Ison, J. and Schwämmle, V  ...  ., Palmblad, M. Schwämmle, V. and Ison J. Community curation of software tools as illustrated for mass spectrometry-based proteomics.  ... 
doi:10.5281/zenodo.1456766 fatcat:hply4krokvfsroveizv3c7pdwi

Scientific workflows for bibliometrics

Arzu Tugce Guler, Cathelijn J. F. Waaijer, Magnus Palmblad
2016 Scientometrics  
Scientific workflows organize the assembly of specialized software into an overall data flow and are particularly well suited for multi-step analyses using different types of software tools. They are also favorable in terms of reusability, as previously designed workflows could be made publicly available through the myExperiment community and then used in other workflows. We here illustrate how scientific workflows and the Taverna workbench in particular can be used in bibliometrics. We discuss
more » ... the specific capabilities of Taverna that makes this software a powerful tool in this field, such as automated data import via Web services, data extraction from XML by XPaths, and statistical analysis and visualization with R. The support of the latter is particularly relevant, as it allows integration of a number of recently developed R packages specifically for bibliometrics. Examples are used to illustrate the possibilities of Taverna in the fields of bibliometrics and scientometrics.
doi:10.1007/s11192-016-1885-6 pmid:27122644 pmcid:PMC4833826 fatcat:u6dfuik24zapln7h4hvm57ldma

iPRG 2019 Metaproteomics Study

Darryl L Davis, Magnus Palmblad, Susan T Weintraub
2019 Journal of Biomolecular Techniques  
Metaproteomics provides a range of technical challenges, from sampling to data analysis. In this study we will investigate where we are with respect to software and pipelines configurable or specially developed for metaproteomics data analysis. The participants will receive label-free LC-MS/MS datasets of two mixed samples of known bacterial species composition, where the bacteria were grown under different conditions. The participants are free to use any software they like to answer one or
more » ... of the following questions: 1) What is the dominant organism in the sample? 2) Which other genera, species and strains can be identified in the sample, and what are their relative abundances? and 3) What could be inferred about differences in the environments from which the two samples were collected? Specific Aims: 1. Where are we as a field when it comes to analyzing data from multiple species? 2. How are taxonomic compositions of samples determined and reported? 3. What can be inferred about adaptation to the environment of the organisms in a sample? In addition to discussing the 2019 Metaproteomics study, there will be time to have a mini workshop on data analysis workflows such as iPython and R markdown.
pmid:31897002 pmcid:PMC6938079 fatcat:ifkeaz2f3zg6zjw2vlxgdrqfp4

Scientific Workflow Management in Proteomics

Jeroen S. de Bruin, André M. Deelder, Magnus Palmblad
2012 Molecular & Cellular Proteomics  
Data processing in proteomics can be a challenging endeavor, requiring extensive knowledge of many different software packages, all with different algorithms, data format requirements, and user interfaces. In this article we describe the integration of a number of existing programs and tools in Taverna Workbench, a scientific workflow manager currently being developed in the bioinformatics community. We demonstrate how a workflow manager provides a single, visually clear and intuitive interface
more » ... to complex data analysis tasks in proteomics, from raw mass spectrometry data to protein identifications and beyond.
doi:10.1074/mcp.m111.010595 pmid:22411703 pmcid:PMC3394934 fatcat:zpiodoscwzcfnpsih6psfuthya

Scientific workflow optimization for improved peptide and protein identification

Sonja Holl, Yassene Mohammed, Olav Zimmermann, Magnus Palmblad
2015 BMC Bioinformatics  
Peptide-spectrum matching is a common step in most data processing workflows for mass spectrometry-based proteomics. Many algorithms and software packages, both free and commercial, have been developed to address this task. However, these algorithms typically require the user to select instrument-and sample-dependent parameters, such as mass measurement error tolerances and number of missed enzymatic cleavages. In order to select the best algorithm and parameter set for a particular dataset,
more » ... depth knowledge about the data as well as the algorithms themselves is needed. Most researchers therefore tend to use default parameters, which are not necessarily optimal. Results: We have applied a new optimization framework for the Taverna scientific workflow management system (http://ms-utils.org/Taverna_Optimization.pdf) to find the best combination of parameters for a given scientific workflow to perform peptide-spectrum matching. The optimizations themselves are non-trivial, as demonstrated by several phenomena that can be observed when allowing for larger mass measurement errors in sequence database searches. On-the-fly parameter optimization embedded in scientific workflow management systems enables experts and non-experts alike to extract the maximum amount of information from the data. The same workflows could be used for exploring the parameter space and compare algorithms, not only for peptide-spectrum matching, but also for other tasks, such as retention time prediction. Conclusion: Using the optimization framework, we were able to learn about how the data was acquired as well as the explored algorithms. We observed a phenomenon identifying many ammonia-loss b-ion spectra as peptides with N-terminal pyroglutamate and a large precursor mass measurement error. These insights could only be gained with the extension of the common range for the mass measurement error tolerance parameters explored by the optimization framework.
doi:10.1186/s12859-015-0714-x pmid:26335531 pmcid:PMC4558836 fatcat:n5bruogtc5axfg4jmtd4ebt4zy

Neuroscience and accelerator mass spectrometry

Magnus Palmblad, Bruce A. Buchholz, Darren J. Hillegonds, John S. Vogel
2005 Journal of Mass Spectrometry  
Accelerator mass spectrometry (AMS) is a mass spectrometric method for quantifying rare isotopes. It has had great impact in geochronology and archaeology and is now being applied in biomedicine. AMS measures radioisotopes such as 3 H, 14 C, 26 Al, 36 Cl and 41 Ca, with zepto-or attomole sensitivity and high precision and throughput, enabling safe human pharmacokinetic studies involving: microgram doses, agents having low bioavailability, or toxicology studies where administered doses must be
more » ... pt low (<1 µg/kg). It is used to study long-term pharmacokinetics, to identify biomolecular interactions, to determine chronic and low-dose effects or molecular targets of neurotoxic substances, to quantify transport across the blood-brain barrier and to resolve molecular turnover rates in the human brain on the timescale of decades. We will here review how AMS is applied in neurotoxicology and neuroscience.
doi:10.1002/jms.734 pmid:15706618 fatcat:hyyumza6enenra5znurxca3tdy

Automated workflow composition in mass spectrometry based proteomics

Magnus Palmblad, Anna-Lena Lamprecht, Jon Ison, Veit Schwämmle, Jonathan Wren
2018 Bioinformatics  
Numerous software utilities operating on mass spectrometry (MS) data are described in the literature and provide specific operations as building blocks for the assembly of on-purpose workflows. Working out which tools and combinations are applicable or optimal in practice is often hard. Thus researchers face difficulties in selecting practical and effective data analysis pipelines for a specific experimental design.
doi:10.1093/bioinformatics/bty646 pmid:30060113 pmcid:PMC6378944 fatcat:ev5w2fvdkvaxzofrfusrmnklx4

Protein expression dynamics during Escherichia Coli glucose-lactose diauxie

Ekaterina Mostovenko, André M Deelder, Magnus Palmblad
2011 BMC Microbiology  
Escherichia coli is a well-studied anaerobic bacteria which is able to regulate metabolic pathways depending on the type of sugar presented in the medium. We have studied the glucose-lactose shift in E. coli at the protein level using a recently developed mass spectrometry platform. Method: Cells were grown in minimal medium containing two sugars (glucose and lactose) and analyzed using novel mass spectrometry cluster. The cluster combines the high resolving power and dynamic range of Fourier
more » ... ansform ion cyclotron resonance (FTICR) for accurate mass measurement and quantitation with multiple ion traps for fast and sensitive tandem mass spectrometry. The protein expression profile was followed in time across the glucose-lactose diauxic shift using label-free quantitation from the FTICR data. Results and Conclusion: The entire dataset was interrogated by KEGG pathway analysis, mapping measured changes in protein abundance onto known metabolic pathways. The obtained results were consistent with previously published gene expression data, with β-galactosidase being the most strongly induced protein during the diauxic shift.
doi:10.1186/1471-2180-11-126 pmid:21631920 pmcid:PMC3121593 fatcat:ngafrgwzdvbnpfy7sqorca4ij4

Non-Uniform Gaussian Blur of Hexagonal Bins in Cartesian Coordinates [article]

Reinier Vleugels, Magnus Palmblad
2020 arXiv   pre-print
However, in one of our use cases, based on previous work (Palmblad, 2019) , the two dimensions do not represent spatial locations as in an map or image, but two different physical variables, with different  ...  implementation for Bokeh using SCOPE and searching Europe PMC for scientific papers mentioning particular techniques from analytical chemistry in their section-tagged materials and methods sections (Palmblad  ... 
arXiv:2005.09941v2 fatcat:63balgtglfgdrnwjwbukuquy5m

"Lossless" compression of high resolution mass spectra of small molecules

Bo Blanckenburg, Yuri E. M. van der Burgt, André M. Deelder, Magnus Palmblad
2010 Metabolomics  
High magnetic field FTICR also has a wide dynamic range (10 4 -10 5 ) (Limbach et al. 1993 , Palmblad et al. 2000 , especially in comparison with other ion trapping instruments.  ...  Additionally, measured isotopic envelopes can be fitted to predicted distributions for confirmation, such as in the Sigma Fit TM algorithm (Bruker Daltonics, Billerica, MA) or a special case of AUTOHD (Palmblad  ... 
doi:10.1007/s11306-010-0202-2 pmid:20676216 pmcid:PMC2899016 fatcat:a5p56qxdrbf6diy6sqxxgtubyq

Combining Text Mining and Computational Chemistry Visually and Semantically Enriches Analytical Chemistry Literature Searches

Magnus Palmblad
2019 Analytical Chemistry  
The open-access scientific literature contains a wealth of information for meaningful text mining. However, this information is not always easy to retrieve. This technical note addresses the problem by a new flexible method combining in a single workflow existing resources for literature searches, text mining, and large-scale prediction of physicochemical and biological properties. The results are visualized as virtual mass spectra, chromatograms, or images in styles new to text mining but
more » ... iar to analytical chemistry. The method is demonstrated on comparisons of analytical-chemistry techniques and semantically enriched searches for proteins and their activities, but it may also be of general utility in experimental design, drug discovery, chemical syntheses, business intelligence, and historical studies. The method is realized in shareable scientific workflows using only freely available data, services, and software that scale to millions of publications and named chemical entities in the literature.
doi:10.1021/acs.analchem.8b05818 pmid:30835438 pmcid:PMC6448173 fatcat:bkantbxvlbaivf2oigbshzk634

iPRG-2020: Proteome Informatics Research Group Study on Metaproteomics

Pratik Jagtap, Susan T. Weintraub, Darryl Davis, Antony Harvey, Michael Hoopmann, Lukas Käll, Samuel H. Payne, Yasset Perez-Riverol, Magnus Palmblad
2021 Zenodo  
Metaproteomics – the characterization of proteins expressed by microbiomes – presents a range of technical challenges, from sampling to data processing and interpretation. In the iPRG 2020 study, we investigated the status of metaproteomics data analysis workflows by posing questions to the metaproteomics studies in two studies. In two phases of the study, the participants were asked to deduce the organisms or taxa in a metaproteomics sample ("What species are represented in the sample?") and
more » ... at biological phenomena have taken place ("What interactions took place between the species in the mixture?"). The outputs from these studies will be presented at the RG session at ABRF 2021.
doi:10.5281/zenodo.4599626 fatcat:mcvv74y5zvaetp3q64dawvvoeq

Comparison of peptide and protein fractionation methods in proteomics

Ekaterina Mostovenko, Chopie Hassan, Janine Rattke, André M. Deelder, Peter A. van Veelen, Magnus Palmblad
2013 EuPA Open Proteomics  
Palmblad). identification and possibly quantitation of more peptides and proteins, including those of lower abundance.  ... 
doi:10.1016/j.euprot.2013.09.001 fatcat:rqtdq54razhbtkeqdpog4ribg4

Mechanistic studies of multipole storage assisted dissociation

Kristina Håkansson, Jan Axelsson, Magnus Palmblad, Per Håkansson
2000 Journal of the American Society for Mass Spectrometry  
The degree and onset of fragmentation in multipole storage assisted dissociation (MSAD) have been investigated as functions of several hexapole parameters. Strict studies of hexapole charge density (number of ions injected) and hexapole storage time were made possible by placing a pulsed shutter in front of the entrance to the mass spectrometer. The results obtained show that the charge density is the most critical parameter, but also dependencies on storage time, radio-frequency (rf)
more » ... , and pressure are seen. From these data, and from simulations of the ion trajectories inside the hexapole, a mechanism for MSAD, similar to the ones for sustained off-resonance irradiation (SORI), and for low energy collisionally induced dissociation in the collision multipole of a triple quadrupole mass spectrometer, is proposed. It is believed that, at higher charge densities, ions are pushed to larger hexapole radii where the electric potential created by the rf field is higher, forcing the ions to oscillate radially to higher amplitudes and thereby reach higher (but still relatively low) kinetic energies. Multiple collisions with residual gas molecules at these elevated energies then heat up the molecules to their dissociation threshold. Further support for this mechanism is obtained from a comparison of MSAD and SORI spectra which are almost identical in appearance. (J Am Soc Mass Spectrom 2000, 11, 210 -217)
doi:10.1016/s1044-0305(99)00144-0 pmid:10697816 fatcat:wmtua7yzmjdhdgzk2ghqmnvnbu
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